User: tobias.kockmann

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Posts by tobias.kockmann

<prev • 24 results • page 1 of 3 • next >
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX Martin! A general question: I am starting to develop a package for dealing with peptide mapping data (data coming from a bottom-up proteomics experiment) and I think the Biostrings and IRanges package could be the basis for this, but I am having trouble to get an overview what functionality is a ...
written 4 days ago by tobias.kockmann10
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX! > real.rl <- as(rl, "RangesList") > class(real.rl) [1] "SimpleRangesList" attr(,"package") [1] "IRanges" Where is that function documented? ...
written 4 days ago by tobias.kockmann10
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how to transform a list of IRanges into a RangesList instance
... Dear bioC support, I have constructed a list of IRanges named rl: > class(rl) [1] "list" > class(rl[[1]]) [1] "IRanges" attr(,"package") [1] "IRanges" Now I realized that there is already a RangesList class in the IRanges package that I could use instead of the "primitive" list. Problem: I ...
rangeslist-class {iranges} written 5 days ago by tobias.kockmann10 • updated 4 days ago by James W. MacDonald42k
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Comment: C: Ranges on AAStrings
... I found two exceptions. findOverlaps() and countOverlaps() work directly on the Views object if queried against itself (within proteins for a AAString subject): hits <- findOverlaps(query = v1, maxgap = 1, drop.self=TRUE, drop.redundant=TRUE) c <- countOverlaps(query = v1, maxgap = 1, drop. ...
written 24 days ago by tobias.kockmann10
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Comment: C: Ranges on AAStrings
... True thought! ...
written 24 days ago by tobias.kockmann10
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Ranges on AAStrings
... Hi BioC, can anyone help me with the following: I mapped a set of peptides (short AA sequences) to a set of proteins using exact string matching. Now, I would like to compare the locations of the mapped peptide to each other, in order to find peptides that locate next to one another. To me this pr ...
biostrings aastring views written 25 days ago by tobias.kockmann10
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Hi Herve, hmmm...I looked at the size of the list of MIndex objects returned and got this: > object.size(m[[1]]) 9458832 bytes In total the list contains 10 of these MIndex objects, so the list of MIndex objects has a total memory footprint of 90 Mb! The corresponding list-of-list structure ...
written 5 weeks ago by tobias.kockmann10
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Oh really! Good to know. What are "hits objects"? The question of the return type is indeed not trivial. The list of MIndex objects returned by vmatchPattern() is not to easy to deal with...at least it is not obvious to me and it looks quite bulky (big memory footprint), because it returns an empty ...
written 6 weeks ago by tobias.kockmann10
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Comment: C: how to catch an error when using subseq() in vectorized way
... Ohhh...I did not know that substr() can process instances of the AAStringSet class, but that is of very useful information. THX! ...
written 6 weeks ago by tobias.kockmann10
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Sorry...vmatchPDict() ...
written 6 weeks ago by tobias.kockmann10

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